Freesurfer

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30070 discussions

over-estimated brain volume based on (recon-all / recon-all-clinical) ?
by Yoonho Hwang 18 Jul '23

18 Jul '23

External Email - Use Caution Dear FS developers, Hi, I am very happy that we can use new features of FreeSurfer (e.g., recon-all-clinical.sh, SynthSeg, SynthSR, etc.) While using a variety of functions from FreeSurfer (v7.3.2 and v7.4.1), we would like to hear the answers to the following questions. 1-1. Compared to the recon-all stream, using SynthSeg seems to overestimate the volume in many subregions of the brain including eTIV? Can you explain why this happens? 1-2. The estimated volume of the entorhinal cortex is different between recon-all/SynthSeg and recon-all-clinical.sh. There is a 3-4 times difference. Can you tell me why the result is? 2. Can the functions (segment_subregions, segmentThalamicNuclei.sh, segmentBA.sh, segmentHA.sh, etc.) used in recon-all be used in recon-all-clinical.sh? Please let me know if there is anything you don't understand. Looking forward to your feedback. Thank you very much. Best, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic Study,* *College of Medicine, Korea University* *#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, **15355, Republic of Korea.* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

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how to manipulate values in m3z file
by Proulx, Jean Sebastien 17 Jul '23

17 Jul '23

External Email - Use Caution Hello, I produced an m3z warp file with mri_gradunwarp. Now I need to 0 out all displacement in the z direction, while keeping everything else the same since I need to combine multiple warps from images with different geometries. I see two strategies: (1) working directly on the m3z file I could not get mri_convert or mris_calc to do the trick. I thought I nailed it by manually editing the m3z file in freeview, but freeview saves the results in mgz format :-( Is there anything else I missed? (2) converting to mgz or nii timeseries, manupulate those and convert back to m3z mri_convert produced a nii file that freeview could not read and a single-frame mgz file that looks like some mishmash of the original 3-frame m3z. Any idea on how I can acheive my goal? A word on why would I want to do this silly thing. I have single-slice EPI and fov-matched higher-inplane-resolution single-slice GRE images. They have different within-slice gradient-non-linearity-related distortions. I want to undistort the GRE image then distort it to the EPI space. I need to zero out through-plane distortions to avoid displacing signal outside the imaging grid. Ignoring through-plane distortions should not be a problem for overlaying my GRE and EPI since, unlike within-plane distorsions, through-plane distortions are matched. Thanks a lot for the help and Have a very good day! Sebastien

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Freesurfer VM .7z Password
by Spencer Chandler 17 Jul '23

17 Jul '23

External Email - Use Caution Hello, I've downloaded the 7.2 Ubuntu virtual machine and its asking for a password to extract it. Is this something I can get? Thank you! -Spencer

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re-running recon-all after aseg.presurf.mgz edits
by Alexopoulos, Dimitrios 17 Jul '23

17 Jul '23

External Email - Use Caution A few quick questions FS experts. I made manual edits on subcortical structures in outputs from FS6.0. Specifically, I made the edits on the aseg.presurf.mgz file. I then reran using: recon-all -s neo267e_nil -autorecon2-noaseg -autorecon3 Do the updated stats files aseg.stats and ?h.aparc.stats incorporate these changes? I ask b/c the mri_segstats cmdline below uses the aseg.mgz not aseg.presurf.mgz # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/pkg/freesurfer6.0/ASegStatsLUT.txt --subject neo267f_nil ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Can I use Freeview (tksurferfv) Tools on surface?
by Andy Kim 17 Jul '23

17 Jul '23

External Email - Use Caution Dear FreeSurfer Developers, Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine voxel draw" of ROI edit tool (https://secure-web.cisco.com/1uYpRPHzaQ-b275n3Qt2rqUmDAbInkPLAno41z_mXOvA9D…) On the other hand, unfortunately, it seems that it only works in 3d volume space. So, I tried "Path/Custom FIll" -> pointing 4 vertices of a rectangle -> "Make Closed Path". But this time, the vertices were not connected straight. The lines were zigzag. Could you tell me how to draw a rectangular ROI with straight lines. Furthermore, if possible, could you explain how zigzag lines form? Thank you in advance. Kind Regards, Andy (Junghyun) Kim

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some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
by zlseu2109 17 Jul '23

17 Jul '23

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu FROM: zlseu2109(a)163.com SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz Hello FreeSurfer Developers, I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2 2) Platform: Ubuntu Release 20.04.6 (focal) | | zlseu2109 | | zlseu2109(a)163.com |

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can't generate 3D rendering
by Magang Visa 16 Jul '23

16 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, i'm attempting to open a 3D freeview but i don't see the 3D rendering i'm using this code to open the file freeview T1.mgz norm.mgz brain.mgz aseg.mgz 1) FreeSurfer version:Version 7 Release is 7.4.1 2) Platform: CentOS thanks [image: image.png]

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Re: [Freesurfer] pop up does not get focus
by fsbuild 16 Jul '23

16 Jul '23

External Email - Use Caution What you report looks like an issue with WSL and not the X-Ming X-server or the fressurfer distribution.  You could try following the advice in the postings below. This posting mentions focus and user input may be getting lost if the window has gone into “select” mode,  stackoverflow.com/questions/53939435/wsl-terminal-forgets-to-update-and-los… This posting recommends disabling Linux GUI support by setting guiapplications=false in your %USERPROFILE%\.wslconfig file.  I’m not sure about this, because I’ve never seen this previously reported or had to try that edit. github.com/microsoft/wslg/issues/443 - R. On Jul 16, 2023, at 15:36, Tsahi Asher <tsahi.asher(a)mail.huji.ac.il> wrote:        External Email - Use Caution        Hello,I have a problem when i use freeview.Setup:Windows 11wsl ubuntu 22.04windows xserver - xming (vcxsrv) 1.20.14.0 with the following parameters<XLaunch WindowMode="MultiWindow" ClientMode="NoClient" LocalClient="False" Display="-1" LocalProgram="xcalc" RemoteProgram="xterm" RemotePassword="" PrivateKey="" RemoteHost="" RemoteUser="" XDMCPHost="" XDMCPBroadcast="False" XDMCPIndirect="False" Clipboard="True" ClipboardPrimary="True" ExtraParams="" Wgl="False" DisableAC="False" XDMCPTerminate="False"/>freesurfer for ubuntu 7.4.1problem:When i use the app some popup windows do not get focused, I have no way to make any button of the popup work, not with the mouse and not with the keyboard, not any button in the popup, but also not main windows buttons (close maximize etc), i also can not drag and move the windows. Attached are two examples from the freeview app. The "load surface overlay" is a pop up that is responding, the "configure overlay" pop up is the one that i can not get to work.Thank you,Tsahi<load.jpg><configure.jpg>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer installation issue
by fsbuild 16 Jul '23

16 Jul '23

External Email - Use Caution  Try using apt to do the install, and you could also preface the package name with its absolute path, /path/to/package $ sudo apt install /path/to/package/freesurfer_7.2.0_amd64.deb - R. On Jul 15, 2023, at 05:02, Ramesh Babu <mgrameshbabu2013(a)gmail.com> wrote:        External Email - Use Caution        Dear Expert,I am trying to install Freesurfer-7.2 .deb package. I had this package earlier, and after formatting my system now, I am trying to install Freesurfer again. But I am facing the following issues. 'freesurfer_7.2.0_amd64.deb' is not a Debian format archivedpkg: error processing archive freesurfer_7.2.0_amd64.deb (--install): dpkg-deb --control subprocess returned error exit status 2Errors were encountered while processing: freesurfer_7.2.0_amd64.debKindly request you to provide a solution to solve this issue.Thanks in advanceRamesh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

pop up does not get focus
by Tsahi Asher 16 Jul '23

16 Jul '23

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